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Computational Software Provides Rapid Identification of Disease-Causing Gene Variations

Computational Software Provides Rapid Identification of Disease-Causing Gene Variations

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Computational Software Provides Rapid Identification of Disease-Causing Gene Variations

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  1. Computational Software Provides Rapid Identification of Disease-Causing Gene Variations ScienceDaily (June 23, 2011) — Scientists from the University of Utah and Omicia, Inc., a privately held company developing tools to interpret personal genome sequences, have announced the publication in Genome Research of a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool -- a probabilistic disease-causing mutation finder for individual human genomes.

  2. Intriguing uses of the power of genomics • Microarray offers us the opportunity to teach DNA structure, function, replication, etc. • So I was thinking………

  3. What do you do with all the information – and better yet, where on earth do I begin?????

  4. Microarrays and SNP analysis: Single nucleotide polymorphisms: In humans, a copy of a T at location rs2472297 was associated with about 0.25 cups more coffee consumed per day. Citation: Sulem P et al. (2011) . “Sequence variants at CYP1A1-CYP1A2 and AHR associate with coffee consumption.” Hum Mol Genet.

  5. Genotype What It Means TT Subjects who drank coffee consumed a slightly higher amount of coffee per day, on average. CT Subjects who drank coffee consumed a slightly higher amount of coffee per day, on average. CC Subjects who drank coffee consumed a typical amount of coffee per day, on average.

  6. So here is where magic happens! My goal is for students to explore this caffeine effect further by mining microarray data already present – there seems to be data in yeast. Ideally, we would obtain some microarrays and do our own experiments – with students setting up the experiment and asking their own questions. This is my big black box right now!

  7. At the end of our gene regulation module in our Genetics 201 labs, my goal is for students to be able to: Understand how microarray data is generated and how it can be used to generate new hypotheses Explore bioinformatics sites and be able to extract information and data from already published work Understand how RT-PCR works and how it is used to study regulation of gene expression Make conclusions about their hypotheses regarding the gene expression changes that might result from caffeine exposure inour model organism and possibly relate that to effects in humans

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